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Analysis of Self-Assembly Monolayer Molecules on Micro-Cantilever using Molecular Dynamics Simulation

Y.T. Wang, Y.C. Shih and H.C. Kan
National Center for High-performance Computing, TW

Keywords:
self-assembly monolayer, micro-cantilever, molecular dynamics simulation

Abstract:
Micro-cantilever can be regarded as a sensing device by measuring its deflection resulting from the binding amounts of targeted samples and coated chemical compounds on its surface. In this work, we compute the change of Gibbs free energy of the Self-Assembled Monolayer (SAM) molecules on the surface of the micro-cantilever and mapped the results to the deflection of the micro-cantilever according to the modified Stoney’s equation. All computations of the free energy changes were performed isothermally with Periodic Boundary Conditions (PBC) by the commercial Molecular Dynamics (MD) simulation software CHARMM in associated with the specific molecular topology and force fields for alkanethiolic molecules CH3(CH2)NSH, N=3, 7, and 11. In the present study, the deflection of the micro-cantilever with an Au(111) layer coated on the upper surface and adsorbed with alkanethiolic molecules, is analyzed. The alkanethiolic molecules are arranged in a specific pattern in the 8x8 array format adsorbed on the Au atoms coated on the surface of the micro-cantilever. The effects of the seeding density of the adsorbed molecules are taken into consideration by different separations between Au atoms.

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